<html>

<head>
<title>Per Base N Content</title>
<style type="text/css">
	body {
		font-family: sans-serif;
	}
</style>
</head>
<body>
<h1>Per Base N Content</h1>
<h2>Summary</h2>
<p>
If a sequencer is unable to make a base call with sufficient confidence
then it will normally substitute an N rather than a conventional base]
call
</p>
<p>
This module plots out the percentage of base calls at each position for
which an N was called.
</p>
<p><img src="per_base_n_content.png"></p>

<p>
It's not unusual to see a very low proportion of Ns appearing in a sequence, 
especially nearer the end of a sequence.  However, if this proportion rises
above a few percent it suggests that the analysis pipeline was unable to
interpret the data well enough to make valid base calls.
</p>

<h2>Warning</h2>
<p>
This module raises a warning if any position shows an N content of >5%.
</p>

<h2>Failure</h2>
<p>
This module will raise an error if any position shows an N content of >20%.
</p>

<h2>Common reasons for warnings</h2>
<p>
The most common reason for the inclusion of significant proportions of Ns
is a general loss of quality, so the results of this module should be evaluated
in concert with those of the various quality modules.  You should check the 
coverage of a specific bin, since it's possible that the last bin in this analysis
could contain very few sequences, and an error could be prematurely triggered in 
this case.
</p>
<p>
Another common scenario is the incidence of a high proportions of N at a small
number of positions early in the library, against a background of generally 
good quality.  Such deviations can occur when you have very biased sequence 
composition in the library to the point that base callers can become confused
and make poor calls.  This type of problem will be apparent when looking at the
per-base sequence content results.
</p>
</body>
</html>
